Abstract
The brown alga, Nemacystus decipiens (“ito-mozuku” in Japanese), is one of the major edible seaweeds, cultivated principally in Okinawa, Japan. N. decipiens is also a significant source of fucoidan, which has various physiological activities. To facilitate brown algal studies, we decoded the ~154 Mbp draft genome of N. decipiens Onna-1 strain. The genome is estimated to contain 15,156 protein-coding genes, ~78% of which are substantiated by corresponding mRNAs. Mitochondrial genes analysis showed a close relationship between N. decipiens and Cladosiphon okamuranus. Comparisons with the C. okamuranus and Ectocarpus siliculosus genomes identified a set of N. decipiens-specific genes. Gene ontology annotation showed more than half of these are classified as molecular function, enzymatic activity, and/or biological process. Extracellular matrix analysis revealed domains shared among three brown algae. Characterization of genes that encode enzymes involved in the biosynthetic pathway for sulfated fucan showed two sets of genes fused in the genome. One is a fusion of l-fucokinase and GDP-fucose pyrophosphorylase genes, a feature shared with C. okamuranus. Another fusion is between an ST-domain-containing gene and an alpha/beta hydrolase gene. Although the function of fused genes should be examined in future, these results suggest that N. decipiens is another promising source of fucoidan.
Highlights
Brown algae comprise many types of seaweeds in oceans and serve important functions in marine ecosystems[1]
The most abundant transcription factors (TFs) occurred in the Myb family, with 79, 74, and 70 genes detected in N. decipiens, C. okamuranus, and E. siliculosus genome, respectively
In order to examine brown algae-unique and Chordariales (N. decipiens and C. okamuranus)-unique extracellular matrix (ECM) components, we searched genes for those possibly associated with the ECM in genomes of the three brown algae, a diatom (Thalassiosira pseudonana), an oocyte (Phytophthora infestans), a green alga (Chlamydomonas reinhardtii), and a land plant (Arabidopsis thaliana), as described in the Materials and Methods. 676, 649, 901, 644, 1,116, 699, and 1,116 genes were defined as putative ECM genes in N. decipiens, C. okamuranus, E. siliculosus, T. pseudonana, P. infestans, C. reinhardtii, and A. thaliana genomes, respectively (Supplementary Tables S7 and S8)
Summary
Brown algae comprise many types of seaweeds in oceans and serve important functions in marine ecosystems[1]. The GC content of the N. decipiens genome was calculated as ~56% (Supplementary Fig. S2B; Table 1), versus 54% for both C. okamuranus and E. siliculosus (Table 1). DNA transposons and www.nature.com/scientificreports retrotransposons accounted for 0.2098% and 2.0143% of the N. decipiens genome, respectively (Supplementary Table S2).
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